Background: Cystic fibrosis (CF) is one of the most common autosomal recessive genetic disorders in pediatrics. Due to inadequate clearance of inhaled pathogens in the mucus, these organisms colonize the airways, leading to inflammatory responses. The microorganisms identified in sputum cultures of CF patients are critical for selecting the appropriate antibiotics for treatment. Objectives: The main aim of this study is to identify the microorganisms colonizing the sputum of patients with CF and to assess the prognostic factors influencing these colonizations. Methods: This study included all cases of CF patients referred to the pediatric pulmonology clinics at Mofid Pediatric Hospital between 2017 and 2022. Demographic and clinical history data were obtained from clinical records and face-to-face interviews. Sputum cultures were performed for all patients. The chi-square test was applied to identify significant differences in qualitative variables. For quantitative variables, the One-Way ANOVA and Student's t-test were used to find significant differences for parametric data. Results: A total of 206 patients participated in the study, with a mean age of 9.8 ± 5.42 years. Pseudomonas aeruginosa (PA) and Staphylococcus aureus (SA) were the most common microorganisms detected, with prevalence rates of 51.94% and 16.99%, respectively. Common microorganisms were more prevalent among patients with normal or below-normal Body Mass Index (BMI), while unusual microorganisms were more frequent in those with above-normal BMI, indicating a significant relationship between microorganism type and BMI (P-value: 0.014). Additionally, common microorganisms were more prevalent in older patients, with a mean age of 10.30 years (P-value = 0.006). No other variables showed statistical significance. Conclusions: PA and SA were the most prevalent microorganisms in the sputum cultures of CF patients. A significant relationship was observed between microorganism type, BMI, and age of the patients.